Question: What is the difference between the gene expression (GEX) and V(D)J reference packages - can we use one instead of the other?
Answer: The GEX and V(D)J references are completely different reference packages and cannot be interchanged.
The GEX reference packages for human and mouse represent the whole transcriptome for each organism and are used for gene expression analysis with the cellranger count pipeline. The cellranger count pipeline is used to analyze both 5' and 3' gene expression assay data. The reference packages can be downloaded here.
The V(D)J references (currently human and mouse only) consist of only V(D)J-specific genes and annotations for each organism in a 10x specific format for the cellranger vdj pipeline. The reference packages can be downloaded here.